Fifteen Years Later: Hard and Soft Selection Sweeps Confirm a Large Population Number for HIV In Vivo

Igor M Rouzine,Leor S Weinberger,John M Coffin,Christophe Fraser

doi:10.1371/journal.pgen.1004179

Abstract

Fifteen Years Later: Hard and Soft Selection Sweeps Confirm a Large Population Number for HIV In Vivo

Highlights

Pennings et al [8] continue this quest for an effective population size of HIV using a new method based on a theoretical calculation of the probability of multiple introductions of a beneficial allele at a site before it is fixed in a population [18]
A linkage disequilibrium (LD) test [12] and analysis of the variation in the time to drug resistance [13] arrived at the same value, Neff = (5–10)6105, for an average patient
The authors use sequence data obtained from 30 patients who failed suboptimal antiretroviral regimens, including efavirenz [19]—a nonnucleoside reverse transcriptase (RT) inhibitor (NNRTI)—and who exhibited a rise of drug-resistant alleles in RT

Summary

Introduction

Pennings et al [8] continue this quest for an effective population size of HIV using a new method based on a theoretical calculation of the probability of multiple introductions of a beneficial allele at a site before it is fixed in a population [18]. Tajima’s ‘‘neutrality test’’ applied to HIV sequences in untreated patients assumed that selection was neutral and predicted much smaller ‘‘effective’’ populations, of Neff,103 [11]. A linkage disequilibrium (LD) test [12] and analysis of the variation in the time to drug resistance [13] arrived at the same value, Neff = (5–10)6105, for an average patient (with the mutation rate ,1025 per base).

Results

Conclusion